I definitely wouldn't expect the game engine to cover some of these strange mechanics, haha! Some of them felt particularly weird or had almost hacked-together solutions (bridge builder is very buggy and hard to get to cooperate, and the solution to Brooke's wood block puzzle on W. Tower F1 feels practically like cheating once you do get it), but I felt like they were interesting enough to include anyways. W. Tower F2 and F3 are probably the hardest just because there's a pretty specific sequence to do things in, and the level can break pretty easily if you miss a step.
Doing a split like this in the main game definitely would be pretty hard. One issue I had a lot when designing was forcing them to stay split even with access to bombs and the destroy magic - in several levels I ended up having to use switches and iron blocks as "indestructible blocks"...having stuff like that hanging around the main levels would confuse a lot of players, I'm sure.